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Protein

High mobility group protein B1

Gene

HMGB1

Organism
Gallus gallus (Chicken)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Multifunctional redox sensitive protein with various roles in different cellular compartments. Nuclear functions are attributed to fully reduced HGMB1. Associates with chromatin and binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA, DNA-containing cruciforms or bent structures, supercoiled DNA and ZDNA. Can bent DNA and enhance DNA flexibility by looping thus providing a mechanism to promote activities on various gene promoters. Can restructure the canonical nucleosome. Proposed to be an universal biosensor for nucleic acids. May promote inflammatory response to sterile and infectious signals and may be involved in the coordination and integration of innate and adaptive immune responses. In the cytoplasm may function as sensor and/or chaperone for immunogenic nucleic acids, and mediate autophagy. May act as danger associated molecular pattern (DAMP) molecule that amplifies immune responses during tissue injury.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei3Involved in intramolecular interaction with the C-terminal acidic tail1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi9 – 79HMG box 1PROSITE-ProRule annotationAdd BLAST71
DNA bindingi95 – 163HMG box 2PROSITE-ProRule annotationAdd BLAST69

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding
Biological processImmunity, Inflammatory response, Innate immunity

Enzyme and pathway databases

ReactomeiR-GGA-211227 Activation of DNA fragmentation factor
R-GGA-5686938 Regulation of TLR by endogenous ligand
R-GGA-6798695 Neutrophil degranulation

Names & Taxonomyi

Protein namesi
Recommended name:
High mobility group protein B1
Alternative name(s):
High mobility group protein 1
Short name:
HMG-1
Gene namesi
Name:HMGB1
Synonyms:HMG1
ORF Names:RCJMB04_15a21
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
Proteomesi
  • UP000000539 Componenti: Chromosome 1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Cytoplasm, Nucleus, Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi3K → A: Impairs binding to distorted DNA; when associated with A-12. 1 Publication1
Mutagenesisi12K → A: Impairs binding to distorted DNA; when associated with A-3. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00004234602 – 215High mobility group protein B1Add BLAST214

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi23 ↔ 45In disulfide HMGB1By similarity
Modified residuei23Cysteine sulfonic acid (-SO3H); alternateBy similarity1
Modified residuei45Cysteine sulfonic acid (-SO3H); alternateBy similarity1
Modified residuei106Cysteine sulfonic acid (-SO3H)By similarity1

Post-translational modificationi

Reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-106 and a possible intramolecular disulfide bond involving Cys-23 and Cys-45 give rise to different redox forms with specific functional activities: 1- fully reduced HMGB1 (HMGB1C23hC45hC106h), 2- disulfide HMGB1 (HMGB1C23-C45C106h) and 3- sulfonyl HMGB1 (HMGB1C23soC45soC106so).By similarity

Keywords - PTMi

Disulfide bond, Oxidation

Proteomic databases

PaxDbiQ9YH06
PRIDEiQ9YH06

Expressioni

Gene expression databases

BgeeiENSGALG00000017082

Interactioni

GO - Molecular functioni

Protein-protein interaction databases

STRINGi9031.ENSGALP00000027541

Structurei

3D structure databases

ProteinModelPortaliQ9YH06
SMRiQ9YH06
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni27 – 43NLS 1By similarityAdd BLAST17
Regioni178 – 184NLS 2By similarity7
Regioni196 – 210Involved in intramolecular interaction with K-3Add BLAST15
Regioni211 – 215Involved in interaction with histone H35

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi27 – 43Nuclear localization signal (NLS) 1By similarityAdd BLAST17
Motifi178 – 184Nuclear localization signal (NLS) 2By similarity7

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi186 – 215Asp/Glu-rich (acidic)Add BLAST30

Domaini

The acidic C-terminal domain forms a flexible structure which can reversibly interact intramolecularily with the HMG boxes and modulate binding to DNA and other proteins; may involve Lys-3 and histone H3 'Lys-37' and 'Lys-38'.By similarity1 Publication

Sequence similaritiesi

Belongs to the HMGB family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0381 Eukaryota
COG5648 LUCA
GeneTreeiENSGT00760000119164
HOGENOMiHOG000197861
HOVERGENiHBG009000
InParanoidiQ9YH06
KOiK10802
OMAiYSQDKRP
OrthoDBiEOG091G0P81
PhylomeDBiQ9YH06
TreeFamiTF105371

Family and domain databases

Gene3Di1.10.30.10, 2 hits
InterProiView protein in InterPro
IPR009071 HMG_box_dom
IPR036910 HMG_box_dom_sf
IPR017967 HMG_boxA_CS
PfamiView protein in Pfam
PF00505 HMG_box, 1 hit
PF09011 HMG_box_2, 1 hit
SMARTiView protein in SMART
SM00398 HMG, 2 hits
SUPFAMiSSF47095 SSF47095, 2 hits
PROSITEiView protein in PROSITE
PS00353 HMG_BOX_1, 1 hit
PS50118 HMG_BOX_2, 2 hits

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9YH06-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKGDPKKPR GKMSSYAFFV QTCREEHKKK HPDASVNFSE FSKKCSERWK
60 70 80 90 100
TMSSKEKGKF EDMAKADKLR YEKEMKNYVP PKGETKKKFK DPNAPKRPPS
110 120 130 140 150
AFFLFCSEFR PKIKGEHPGL SIGDVAKKLG EMWNNTAADD KQPYEKKAAK
160 170 180 190 200
LKEKYEKDIA AYRAKGKVDA GKKVVAKAEK SKKKKEEEED EDEDEEDEED
210
EEEEEEEEED DDDDE
Length:215
Mass (Da):24,909
Last modified:May 1, 1999 - v1
Checksum:i3731F50262DCB1C3
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti214Missing in AAD52670 (PubMed:10978508).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y17968 mRNA Translation: CAA76978.1
AJ851648 mRNA Translation: CAH65282.1
AF178849 Genomic DNA Translation: AAD52670.1
AADN03000868 Genomic DNA No translation available.
AADN03001640 Genomic DNA No translation available.
JQ040530 mRNA Translation: AFD33645.1
RefSeqiNP_990233.1, NM_204902.2
XP_015133153.1, XM_015277667.1
XP_015133156.1, XM_015277670.1
UniGeneiGga.4638

Genome annotation databases

EnsembliENSGALT00000062837; ENSGALP00000047606; ENSGALG00000042875
ENSGALT00000075072; ENSGALP00000044781; ENSGALG00000042875
GeneIDi395724
KEGGigga:395724

Similar proteinsi

Entry informationi

Entry nameiHMGB1_CHICK
AccessioniPrimary (citable) accession number: Q9YH06
Secondary accession number(s): H9BNX0, Q9PUK9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 18, 2013
Last sequence update: May 1, 1999
Last modified: April 25, 2018
This is version 123 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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